PDXB_ECOLI
ID PDXB_ECOLI Reviewed; 378 AA.
AC P05459;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1990, sequence version 2.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Erythronate-4-phosphate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_01825};
DE EC=1.1.1.290 {ECO:0000255|HAMAP-Rule:MF_01825};
GN Name=pdxB {ECO:0000255|HAMAP-Rule:MF_01825};
GN OrderedLocusNames=b2320, JW2317;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=2681152; DOI=10.1128/jb.171.11.6084-6092.1989;
RA Schoenlein P.V., Roa B.B., Winkler M.E.;
RT "Divergent transcription of pdxB and homology between the pdxB and serA
RT gene products in Escherichia coli K-12.";
RL J. Bacteriol. 171:6084-6092(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 273-378.
RC STRAIN=K12;
RX PubMed=2991861; DOI=10.1093/nar/13.14.5297;
RA Arps P.J., Marvel C.C., Rubin B.C., Tolan D.A., Penhoet E.E., Winkler M.E.;
RT "Structural features of the hisT operon of Escherichia coli K-12.";
RL Nucleic Acids Res. 13:5297-5315(1985).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 273-378.
RC STRAIN=K12;
RX PubMed=3029016; DOI=10.1128/jb.169.3.1061-1070.1987;
RA Arps P.J., Winkler M.E.;
RT "Structural analysis of the Escherichia coli K-12 hisT operon by using a
RT kanamycin resistance cassette.";
RL J. Bacteriol. 169:1061-1070(1987).
RN [7]
RP PATHWAY.
RX PubMed=8595869; DOI=10.1111/j.1574-6968.1996.tb08001.x;
RA Zhao G., Winkler M.E.;
RT "4-phospho-hydroxy-L-threonine is an obligatory intermediate in pyridoxal
RT 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12.";
RL FEMS Microbiol. Lett. 135:275-280(1996).
RN [8]
RP PYRIDOXAL PHOSPHATE PATHWAY.
RX PubMed=9696782; DOI=10.1128/jb.180.16.4294-4299.1998;
RA Yang Y., Zhao G., Man T.-K., Winkler M.E.;
RT "Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in
RT pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12.";
RL J. Bacteriol. 180:4294-4299(1998).
RN [9]
RP INDUCTION.
RX PubMed=11844765; DOI=10.1128/jb.184.5.1359-1369.2002;
RA Pease A.J., Roa B.R., Luo W., Winkler M.E.;
RT "Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB
RT genes of Escherichia coli K-12.";
RL J. Bacteriol. 184:1359-1369(2002).
CC -!- FUNCTION: Catalyzes the oxidation of erythronate-4-phosphate to 3-
CC hydroxy-2-oxo-4-phosphonooxybutanoate. {ECO:0000255|HAMAP-
CC Rule:MF_01825}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-
CC phosphooxybutanoate + H(+) + NADH; Xref=Rhea:RHEA:18829,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:58538, ChEBI:CHEBI:58766; EC=1.1.1.290;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01825};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis;
CC pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 2/5.
CC {ECO:0000255|HAMAP-Rule:MF_01825, ECO:0000269|PubMed:8595869}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01825}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01825}.
CC -!- INDUCTION: During growth rate. {ECO:0000269|PubMed:11844765}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. PdxB subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_01825}.
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DR EMBL; M29962; AAA24308.1; -; Genomic_DNA.
DR EMBL; U76961; AAB36530.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75380.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16177.1; -; Genomic_DNA.
DR EMBL; X02743; CAA26520.1; -; Genomic_DNA.
DR EMBL; M15541; AAA24310.1; -; Genomic_DNA.
DR PIR; JV0051; DEECPP.
DR RefSeq; NP_416823.1; NC_000913.3.
DR RefSeq; WP_000699148.1; NZ_LN832404.1.
DR AlphaFoldDB; P05459; -.
DR SMR; P05459; -.
DR BioGRID; 4259616; 24.
DR DIP; DIP-10449N; -.
DR IntAct; P05459; 9.
DR STRING; 511145.b2320; -.
DR jPOST; P05459; -.
DR PaxDb; P05459; -.
DR PRIDE; P05459; -.
DR EnsemblBacteria; AAC75380; AAC75380; b2320.
DR EnsemblBacteria; BAA16177; BAA16177; BAA16177.
DR GeneID; 946785; -.
DR KEGG; ecj:JW2317; -.
DR KEGG; eco:b2320; -.
DR PATRIC; fig|1411691.4.peg.4413; -.
DR EchoBASE; EB0686; -.
DR eggNOG; COG0111; Bacteria.
DR HOGENOM; CLU_019796_4_0_6; -.
DR InParanoid; P05459; -.
DR OMA; SAPGCNA; -.
DR PhylomeDB; P05459; -.
DR BioCyc; EcoCyc:ERYTHRON4PDEHYDROG-MON; -.
DR BioCyc; MetaCyc:ERYTHRON4PDEHYDROG-MON; -.
DR BRENDA; 1.1.1.290; 2026.
DR UniPathway; UPA00244; UER00310.
DR PRO; PR:P05459; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0033711; F:4-phosphoerythronate dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0051287; F:NAD binding; IDA:EcoCyc.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0036001; P:'de novo' pyridoxal 5'-phosphate biosynthetic process; IMP:EcoCyc.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IMP:EcoCyc.
DR CDD; cd12158; ErythrP_dh; 1.
DR Gene3D; 3.30.1370.170; -; 1.
DR HAMAP; MF_01825; PdxB; 1.
DR InterPro; IPR006139; D-isomer_2_OHA_DH_cat_dom.
DR InterPro; IPR029753; D-isomer_DH_CS.
DR InterPro; IPR029752; D-isomer_DH_CS1.
DR InterPro; IPR006140; D-isomer_DH_NAD-bd.
DR InterPro; IPR020921; Erythronate-4-P_DHase.
DR InterPro; IPR024531; Erythronate-4-P_DHase_dimer.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR038251; PdxB_dimer_sf.
DR Pfam; PF00389; 2-Hacid_dh; 1.
DR Pfam; PF02826; 2-Hacid_dh_C; 1.
DR Pfam; PF11890; DUF3410; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR PROSITE; PS00065; D_2_HYDROXYACID_DH_1; 1.
DR PROSITE; PS00671; D_2_HYDROXYACID_DH_3; 1.
PE 2: Evidence at transcript level;
KW Cytoplasm; NAD; Oxidoreductase; Pyridoxine biosynthesis;
KW Reference proteome.
FT CHAIN 1..378
FT /note="Erythronate-4-phosphate dehydrogenase"
FT /id="PRO_0000075975"
FT ACT_SITE 208
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT ACT_SITE 237
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT ACT_SITE 254
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 45
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 66
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 146
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 232
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 257
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 258
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
SQ SEQUENCE 378 AA; 41368 MW; 6CEF17691CF2C14A CRC64;
MKILVDENMP YARDLFSRLG EVTAVPGRPI PVAQLADADA LMVRSVTKVN ESLLAGKPIK
FVGTATAGTD HVDEAWLKQA GIGFSAAPGC NAIAVVEYVF SSLLMLAERD GFSLYDRTVG
IVGVGNVGRR LQARLEALGI KTLLCDPPRA DRGDEGDFRS LDELVQRADI LTFHTPLFKD
GPYKTLHLAD EKLIRSLKPG AILINACRGA VVDNTALLTC LNEGQKLSVV LDVWEGEPEL
NVELLKKVDI GTSHIAGYTL EGKARGTTQV FEAYSKFIGH EQHVALDTLL PAPEFGRITL
HGPLDQPTLK RLVHLVYDVR RDDAPLRKVA GIPGEFDKLR KNYLERREWS SLYVICDDAS
AASLLCKLGF NAVHHPAR
